Hello,

I am attempting to modify TPMAP files and then back-convert them to BPMAP
files using the writeTpmap {affxparser} command.

To start, I attempted to convert BPMAP to TPMAP and back to BPMAP using an
Affymetrix BPMAP file which I know can work with my CEL files.

But when I try to use the back-converted file to process my tiling array CEL
files, I get this error:

[1] "WARNING: The input CEL file suggests a different platform than the
PBMAP file."
[1] "CEL platform: 'At35b_MR_v04'"
[1] "BPMAP filename: 'tmp.bpmap'"
Error in AnalyzeTilingCelFiles(CEL.NAMES, bf, outfilename = "btmp.tsv",  :
  ERROR!! Wrong BPMAP file?!  Exiting!

It appears that a BPMAP file created via writeTpmap and tpmap2bpmap is
incompatible with the AnalyzeTilingCelFiles function. What am I doing wrong?

Here is the code I am trying to run:

library(Biobase)
library(affy)
library(preprocessCore)
library(affxparser)
library(AffyTiling)

# original obsolete BPMAP from Affymetrix
of = 'At35b_MR_v04-2_TIGRv5.bpmap'

# TPMAP
tf = 'tmp.tpmap'

# BPMAP
bf = 'tmp.bpmap'

bpmap = readBpmap(of)

# write it in text format
writeTpmap(tf,bpmap,verbose=1)

# convert it back to BPMAP
tpmap2bpmap(tf,bf,verbose=1)

# these are from GSE9646
CEL.NAMES =
  c("GSM243682.CEL",
    "GSM243683.CEL",
    "GSM243684.CEL",
    "GSM243685.CEL")

# the original works fine
AnalyzeTilingCelFiles(CEL.NAMES,of,outfilename="otmp.tsv",readOnlyNCBI=FALSE)


# now try to use the new one
AnalyzeTilingCelFiles(CEL.NAMES,bf,outfilename="btmp.tsv",readOnlyNCBI=FALSE)

Sincerely,

Ann Loraine

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